This has happened to me twice on three completely different Mac Server systems. I had a FMS 12v1 or v2 server on a Mac OS X Server 10.8 and I downloaded the upgrade to FMS 12v3. At the same time I also went through the upgrade to Java 7. After the Java 7 upgrade, I then run the FMS 12v3 updater and everything upgrades fine and there are no warnings of problems. However, when I go and check on Schedules, I find that no scripts can run. When I look at the logs, I get this error every time script tries to run:

I follow the instructions and go to Terminal and try to start FMSE with the "fmsadmin start fmse" command and it does not work. From the Admin Console I try stopping and restarting the FMS service and web publishing to no avail. I restart the entire server and it changes nothing and the FileMaker Script Engine does not work.

I then have to stop the database, export scripts/groups, uninstall FMS 12v3, reinstall FMS 12v1, and then run the upgrade again. After the complete reinstall, the FileMaker Script Engine works just fine.